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1.
Cell ; 2020 Mar 26.
Artigo em Inglês | MEDLINE | ID: mdl-32220310

RESUMO

The ongoing pandemic of a new human coronavirus, SARS-CoV-2, has generated enormous global concern. We and others in China were involved in the initial genome sequencing of the virus. Herein, we describe what genomic data reveal about the emergence SARS-CoV-2 and discuss the gaps in our understanding of its origins.

2.
J Vet Diagn Invest ; 32(2): 287-290, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32065061

RESUMO

Clostridium botulinum is an important pathogen that causes botulism in humans and animals worldwide. C. botulinum group III strains, which produce a single toxin of type C or D or a chimeric toxin of type C/D or D/C, are responsible for botulism in a wide range of animal species including cattle and birds. We used unbiased high-throughput RNA sequencing (i.e., metatranscriptomics) to identify a strain of group III C. botulinum from a deceased Mongolian wild ass (Equus hemionus). The strain was closely related to some European strains. Genetic analysis of the recovered bacterial sequences showed that the C. botulinum strain identified might represent a type C/D strain of group III. Infection by C. botulinum producing the mosaic toxin of type C/D is the most likely cause of the death of the wild ass.

3.
Nature ; 579(7798): 265-269, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32015508

RESUMO

Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health1-3. Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here 'WH-Human 1' coronavirus (and has also been referred to as '2019-nCoV'). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China5. This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.


Assuntos
Betacoronavirus/classificação , Doenças Transmissíveis Emergentes/complicações , Doenças Transmissíveis Emergentes/virologia , Infecções por Coronavirus/complicações , Infecções por Coronavirus/virologia , Pneumonia Viral/complicações , Pneumonia Viral/virologia , Síndrome Respiratória Aguda Grave/etiologia , Síndrome Respiratória Aguda Grave/virologia , Adulto , Betacoronavirus/genética , China , Doenças Transmissíveis Emergentes/diagnóstico por imagem , Doenças Transmissíveis Emergentes/patologia , Infecções por Coronavirus/diagnóstico por imagem , Infecções por Coronavirus/patologia , Genoma Viral/genética , Humanos , Pulmão/diagnóstico por imagem , Masculino , Filogenia , Pneumonia Viral/diagnóstico por imagem , Pneumonia Viral/patologia , RNA Viral/genética , Recombinação Genética/genética , Síndrome Respiratória Aguda Grave/diagnóstico por imagem , Síndrome Respiratória Aguda Grave/patologia , Tomografia Computadorizada por Raios X , Sequenciamento Completo do Genoma
5.
Viruses ; 11(12)2019 Nov 25.
Artigo em Inglês | MEDLINE | ID: mdl-31775324

RESUMO

DNA viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of sampling of DNA viruses from invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA viruses, and herein we used this methodology to identify actively transcribing DNA viruses in meta-transcriptomic libraries of diverse invertebrate species. Our analysis revealed high levels of phylogenetic diversity in DNA viruses, including 13 species from the Parvoviridae, Circoviridae, and Genomoviridae families of single-stranded DNA virus families, and six double-stranded DNA virus species from the Nudiviridae, Polyomaviridae, and Herpesviridae, for which few invertebrate viruses have been identified to date. By incorporating the sequence of a "blank" experimental control we also highlight the importance of reagent contamination in metagenomic studies. In sum, this work expands our knowledge of the diversity and evolution of DNA viruses and illustrates the utility of meta-transcriptomic data in identifying organisms with DNA genomes.

6.
Pediatr Infect Dis J ; 38(11): 1079-1084, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31568248

RESUMO

BACKGROUND: Hand, foot and mouth disease (HFMD) is caused mostly by enteroviruses. However, other viral agents also can cause similar syndromes, and hence, the infections they cause are often misdiagnosed clinically. To determine non-enterovirus etiologic agents in HFMD-like cases, we screened enterovirus-negative samples collected from the patients who were clinically diagnosed as HFMD in China. METHODS: Two hundred enterovirus-negative samples were collected previously in Wenzhou city of Zhejiang province, China. Both high throughput sequencing and RT-PCR were used to screen viral agents. In addition, their clinical features were analyzed. RESULTS: Norovirus (NoV) and human parechovirus (HPeV) were identified from 22 (11.00%) and 9 (4.50%) samples, respectively. In addition, the complete genome sequences were recovered from 4 NoV-positive samples, and the VP1/3Dpol gene sequences were recovered from 5 HPeV-positive samples. Phylogenetic analyses of the NoV sequences revealed that they were closely related to those circulated in other regions of China. Notably, 4 genotypes of HPeVs, including HPeV-1, HPeV-4, HPeV-5 and HPeV-14, were found, indicating high genetic diversity of the virus. Frequent recombination between various genotypes was also observed in the HPeVs. Although most of the patients presented with the clinical features of HFMD, 4 patients infected with NoV GII.4 and 3 patients infected with HPeV-1 (1) and HPeV-4 (2) were characterized with diarrhea. Finally, tonsillitis, convulsion and granulocytopenia were observed in 1 NoV GII.4 patient, while liver dysfunction was found in 1 NoV GII.17 patient. CONCLUSIONS: These data reveal the variety of agents in the cases clinically diagnosed as HFMD.

7.
Sci Rep ; 9(1): 13176, 2019 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-31511528

RESUMO

Diseases caused by Rickettsiales bacteria are a global public health problem. To better understand the diversity and origins of Rickettsiales infection in humans and animals, we sampled 134 febrile patients, 173 rodents and 43 shrews, as well as 358 ticks, from two cities in Jiangsu and Jiangxi provinces, China. Our data revealed a relatively high prevalence of scrub typhus cases in both localities. In addition, both serological tests and genetic analysis identified three patients infected with Anaplasma bovis, Rickettsia monacensis, and Orientia tsutsugamushi bacteria. Molecular epidemiological investigation revealed the co-circulation of multiple species of Rickettsiales bacteria in small mammals and ticks in both provinces, potentially including novel bacterial species. In sum, these data demonstrate the ongoing importance of Rickettsiales infection in China and highlight the need for the regular surveillance of local arthropods, mammals and humans.

8.
Infect Genet Evol ; 75: 104012, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31446137

RESUMO

Although most of Arvicolinae associated hantaviruses can not cause disease in humans, hemorrhagic fever with renal syndrome (HFRS) cases caused by Tula virus (TULV) have been described in Europe since 2002. In addition to Europe, TULV was also identified in the Microtus arvalis obscurus voles sampled from Kazakhstan, which shares borders with China. To gain more insight into the molecular epidemiology of TULV, a total of 365 rodents representing 7 species of 4 subfamily (Arvicolinae, Murinae, Gerbillinae, and Cricetinae) were captured in Qapqal county, Xinjiang, northwest China. Hantavirus RNA was recovered from 40 lung tissue samples of M. arvalis obscurus, with the prevalence of 10.96%. Genetic analysis revealed that all recovered viral sequences were most closely related to those of TULV, but exhibited >11% nucleotide differences from all currently known TULV, suggesting that they may represent a new subtype of TULV. In the S tree, the newly identified viruses formed a distinct lineage and showed a close evolutionary relationship with those sampled from Southwestern Siberia and Kazakhstan. However, they exhibited a different clustering pattern in both the M and the L trees, suggesting the possibility of genetic reassortment. Finally, the recombination event was also observed in Xinjiang TULV viruses. In sum, all these data reveal a complex evolutionary history of TULV in Central Asia.

9.
Virus Res ; 272: 197717, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31422116

RESUMO

Insectivores are the new emerging reservoir of hantaviruses. Here, we describe Lena virus (LENV), a novel hantavirus harbored by the Laxmann`s shrew (Sorex caecutiens), which is also the host of Artybash virus (ARTV). Genetic analysis of the complete genomic sequence shows that LENV is in distant relation to ARTV and other Sorex-borne hantaviruses, suggesting that LENV has emerged from cross-species transmission. Additionally, new genetic variant of ARTV, designated as ARTV-St, was identified in tundra shrews (Sorex tundrensis). Finally, distinct insectivore-borne hantaviruses are co-circulating in the same localities of far eastern Russia: LENV, ARTV and Yakeshi in the forest site, while ARTV, ARTV-St, and Kenkeme virus in the meadow field site.

10.
Cancer Med ; 8(8): 4055-4069, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31150167

RESUMO

BACKGROUND: Most lung cancer patients are diagnosed after the onset of symptoms. However, whether the symptoms of lung cancer were independently associated with the diagnosis of lung cancer is unknown, especially in the Chinese population. METHODS: We conducted a 10 years (2005-2014) nationwide multicenter retrospective clinical epidemiology study of lung cancer patients diagnosed in China. As such, this study focused on nonsmall cell lung cancer (NSCLC). We calculated the odds ratios (ORs) for variables associated with the symptoms and physical signs using multivariate unconditional logistic regressions. RESULTS: A total of 7184 lung cancer patients were surveyed; finally, 6398 NSCLC patients with available information about their symptoms and physical signs were included in this analysis. The most common initial symptom and physical sign was chronic cough (4156, 65.0%), followed by sputum with blood (2110, 33.0%), chest pain (1146, 17.9%), shortness of breath (1090, 17.0%), neck and supraclavicular lymphadenectasis (629, 9.8%), weight loss (529, 8.3%), metastases pain (378, 5.9%), fatigue (307, 4.8%), fever (272, 4.3%), and dyspnea (270, 4.2%). Patients with squamous carcinoma and stage III disease were more likely to present with chronic cough (P < 0.0001) and sputum with blood (P < 0.0001) than patients with other pathological types and clinical stages, respectively. Metastases pain (P < 0.0001) and neck and supraclavicular lymphadenectasis (P = 0.0006) were more likely to occur in patients with nonsquamous carcinoma than in patients with other carcinomas. Additionally, patients with stage IV disease had a higher percentage of chest pain, shortness of breath, dyspnea, weight loss, and fatigue than patients with other stages of disease. In multivariable logistic analyses, compared with patients with adenocarcinoma, patients with squamous carcinoma were more likely to experience symptoms (OR = 2.885, 95% confidence interval [CI] 2.477-3.359) but were less likely to present physical signs (OR = 0.844, 95% CI 0.721-0.989). The odds of having both symptoms and physical signs were higher in patients with late-stage disease than in those with early-stage disease (P < 0.0001). CONCLUSIONS: The symptoms and physical signs of lung cancer were associated with the stage and pathological diagnosis of NSCLC. Patients with squamous carcinoma were more likely to develop symptoms, but not signs, than patients with adenocarcinoma. The more advanced the stage at diagnosis, the more likely that symptoms or physical signs are to develop. Further prospective cohort studies are needed to explore these results.

11.
Annu Rev Virol ; 6(1): 119-139, 2019 09 29.
Artigo em Inglês | MEDLINE | ID: mdl-31100994

RESUMO

Although viruses comprise the most abundant genetic material in the biosphere, to date only several thousand virus species have been formally defined. Such a limited perspective on virus diversity has in part arisen because viruses were traditionally considered only as etiologic agents of overt disease in humans or economically important species and were often difficult to identify using cell culture. This view has dramatically changed with the rise of metagenomics, which is transforming virus discovery and revealing a remarkable diversity of viruses sampled from diverse cellular organisms. These newly discovered viruses help fill major gaps in the evolutionary history of viruses, revealing a near continuum of diversity among genera, families, and even orders of RNA viruses. Herein, we review some of the recent advances in our understanding of the RNA virosphere that have stemmed from metagenomics, note future directions, and highlight some of the remaining challenges to this rapidly developing field.

12.
Virology ; 531: 162-170, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30884426

RESUMO

Limited sampling means that relatively little is known about the diversity and evolutionary history of mammalian members of the Hepadnaviridae (genus Orthohepadnavirus). An important case in point are shrews, the fourth largest group of mammals, but for which there is limited knowledge on the role they play in viral evolution and emergence. Here, we report the discovery of a novel shrew hepadnavirus. The newly discovered virus, denoted shrew hepatitis B virus (SHBV), is divergent to be considered a new species of Orthohepadnavirus. Phylogenetic analysis revealed that these viruses were usually most closely related to TBHBV (tent-making bat hepatitis B virus), known to be able to infect human hepatocytes, and had a similar genome structure, although SHBV fell in a more basal position in the surface protein phylogeny. In sum, these data suggest that shrews are natural hosts for hepadnaviruses and may have played an important role in their long-term evolution.


Assuntos
Evolução Molecular , Infecções por Hepadnaviridae/veterinária , Infecções por Hepadnaviridae/virologia , Hepadnaviridae/isolamento & purificação , Musaranhos/virologia , Sequência de Aminoácidos , Animais , China , Genoma Viral , Hepadnaviridae/química , Hepadnaviridae/classificação , Hepadnaviridae/genética , Infecções por Hepadnaviridae/transmissão , Hepatócitos/virologia , Humanos , Orthohepadnavirus/classificação , Orthohepadnavirus/genética , Orthohepadnavirus/isolamento & purificação , Filogenia , Alinhamento de Sequência , Musaranhos/classificação , Proteínas Virais/química , Proteínas Virais/genética
13.
Thorac Cancer ; 10(4): 708-714, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30737899

RESUMO

BACKGROUND: The study was conducted to examine changes in diagnostic and staging imaging methods for lung cancer in China over a 10-year period and to determine the relationships between such changes and socioeconomic development. METHODS: This was a hospital-based, nationwide, multicenter retrospective study of primary lung cancer cases. The data were extracted from the 10-year primary lung cancer databases at eight tertiary hospitals from various geographic areas in China. The chi-squared test was used to assess the differences and the Cochran-Armitage trend test was used to estimate the trends of changes. RESULTS: A total of 7184 lung cancer cases were analyzed. Over the 10-year period, the utilization ratio of diagnostic imaging methods, such as chest computed tomography (CT) and chest magnetic resonance imaging (MRI), increased from 65.79% to 81.42% and from 0.73% to 1.96%, respectively, while the utilization ratio of chest X-ray declined from 50.15% to 30.93%. Staging imaging methods, such as positron emission tomography-CT, neck ultrasound, brain MRI, bone scintigraphy, and bone MRI increased from 0.73% to 9.29%, 22.95% to 47.92%, 8.77% to 40.71%, 42.40% to 62.22%, and 0.88% to 4.65%, respectively; abdominal ultrasound declined from 83.33% to 59.9%. These trends were more notable in less developed areas than in areas with substantial economic development. CONCLUSION: Overall, chest CT was the most common radiological diagnostic method for lung cancer in China. Imaging methods for lung cancer tend to be used in a diverse, rational, and regionally balanced manner.

15.
Lung Cancer ; 128: 91-100, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30642458

RESUMO

OBJECTIVES: This study aimed to explore the clinical profile and its trajectory of lung cancer on clinicopathological characteristics and medical service utilization in China. METHODS: Patients diagnosed with primary lung cancer in tertiary hospitals during 2005-14 were selected from seven geographic regions of China. Data on clinical characteristics and medical service utilization was extracted from medical record, and the ten-year trends were explored. RESULTS: A total of 7184 patients were included, the mean age was 58.3 years and the male-to-female-ratio was 2.7. From 2005 to 2014, the proportion of ≥60 year-old patients increased from 41.2% to 56.2% (p < 0.001). The smoking rate decreased from 62.9% to 51.1% (p < 0.001) and the proportion of females increased from 23.5% to 31.9% (p < 0.001). The proportion of advanced stage increased from 41.9% to 47.4% (p < 0.001). Adenocarcinoma's proportion increased from 36.4% to 53.5% (p < 0.001) while that of squamous carcinoma decreased from 45.4% to 34.4% (p < 0.001). The application of chest X-ray dropped from 50.2% to 31.0% (p < 0.001) but that of chest CT increased from 65.8% to 81.4% (p < 0.001). As two main treatment options, chemotherapy (p = 0.290) and surgery (p = 0.497) remained stable. The medical expenditure per patient increased from 40,508 to 66,020 Chinese Yuan (p < 0.001). CONCLUSIONS: The sustaining high smoking exposure, increasing proportion of female patients, advancing clinical stage, shifting of predominant pathology and increasing medical expenditure demonstrate potential challenges and directions on lung cancer prevention and control in China. Despite substantial changes of clinical characteristics, main treatment options remained unchanged, which needs further investigation.


Assuntos
Neoplasias Pulmonares/epidemiologia , Aceitação pelo Paciente de Cuidados de Saúde , Adulto , Idoso , Idoso de 80 Anos ou mais , China/epidemiologia , Projetos de Pesquisa Epidemiológica , Feminino , Gastos em Saúde , História do Século XXI , Humanos , Neoplasias Pulmonares/diagnóstico , Neoplasias Pulmonares/história , Neoplasias Pulmonares/terapia , Masculino , Programas de Rastreamento , Pessoa de Meia-Idade , Gradação de Tumores , Metástase Neoplásica , Estadiamento de Neoplasias , Estudos Retrospectivos , Fatores de Risco , Classe Social , Inquéritos e Questionários , Fatores de Tempo
16.
Curr Opin Virol ; 31: 9-16, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-30114593

RESUMO

Despite a substantial increase in our knowledge of the biodiversity and evolution of vertebrate RNA viruses, far less is known about the diversity, evolution and origin of RNA viruses across the diverse phylogenetic range of viruses, and particularly in healthy animals that are often only rarely utilized for virological sampling. Fortunately, recent advances in virus discovery using metagenomic approaches are beginning to reveal a multitude of RNA viruses in vertebrates other than birds and mammals. In particular, fish harbor a remarkable array of RNA viruses, including the relatives of important pathogens. In addition, despite frequent cross-species transmission, the RNA viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years.


Assuntos
Evolução Biológica , Variação Genética , Interações entre Hospedeiro e Microrganismos , Vírus de RNA/genética , Vertebrados/virologia , Animais , Biodiversidade , Aves/virologia , Peixes/virologia , Genoma Viral , Humanos , Filogenia
17.
Nature ; 561(7722): E6, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-29946168

RESUMO

Change history: In this Article, author Li Liu should be associated with affiliation number 5 (College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China), rather than affiliation number 4 (Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang, China). This has been corrected online.

18.
Nature ; 556(7700): 197-202, 2018 04.
Artigo em Inglês | MEDLINE | ID: mdl-29618816

RESUMO

Our understanding of the diversity and evolution of vertebrate RNA viruses is largely limited to those found in mammalian and avian hosts and associated with overt disease. Here, using a large-scale meta-transcriptomic approach, we discover 214 vertebrate-associated viruses in reptiles, amphibians, lungfish, ray-finned fish, cartilaginous fish and jawless fish. The newly discovered viruses appear in every family or genus of RNA virus associated with vertebrate infection, including those containing human pathogens such as influenza virus, the Arenaviridae and Filoviridae families, and have branching orders that broadly reflected the phylogenetic history of their hosts. We establish a long evolutionary history for most groups of vertebrate RNA virus, and support this by evaluating evolutionary timescales using dated orthologous endogenous virus elements. We also identify new vertebrate-specific RNA viruses and genome architectures, and re-evaluate the evolution of vector-borne RNA viruses. In summary, this study reveals diverse virus-host associations across the entire evolutionary history of the vertebrates.


Assuntos
Evolução Molecular , Filogenia , Vírus de RNA/classificação , Vírus de RNA/isolamento & purificação , Vertebrados/classificação , Vertebrados/virologia , Anfíbios/virologia , Animais , Biodiversidade , Peixes/virologia , Genoma Viral/genética , Interações Hospedeiro-Patógeno , Vírus de RNA/genética , Répteis/virologia , Transcriptoma
19.
Cell ; 172(6): 1168-1172, 2018 03 08.
Artigo em Inglês | MEDLINE | ID: mdl-29522738

RESUMO

We know less about viruses than any other lifeform. Fortunately, metagenomics has led to a massive expansion in the known diversity of the virosphere. Here, we discuss how metagenomics has changed our understanding of RNA viruses and present some of the remaining challenges, including characterization of the "dark matter" of divergent viral genomes.


Assuntos
Variação Genética , Genoma Viral/genética , Metagenômica/métodos , Vírus/genética , Evolução Molecular , Filogenia , Vírus de RNA/classificação , Vírus de RNA/genética , Vírus/classificação
20.
Virology ; 514: 88-97, 2018 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-29153861

RESUMO

To better understand the evolution of hepadnaviruses, we sampled bats from Guizhou, Henan and Zhejiang provinces, China, and rodents from Zhejiang province. Genetically diverse hepadnaviruses were identified in a broad range of bat species, with an overall prevalence of 13.3%. In contrast, no rodent hepadnaviruses were identified. The newly discovered bat hepadnaviruses fell into two distinct phylogenetic groups. The viruses within the first group exhibited high diversity, with some closely related to viruses previously identified in Yunnan province. Strikingly, the newly discovered viruses sampled from Jiyuan city in the second phylogenetic group were most closely related to those found in bats from West Africa, suggestive of a long-term association between bats and hepadnaviruses. A co-phylogenetic analysis revealed frequent cross-species transmission among bats from different species, genera, and families. Overall, these data suggest that there are likely few barriers to the cross-species transmission of bat hepadnaviruses.


Assuntos
Quirópteros/virologia , Evolução Molecular , Variação Genética , Infecções por Hepadnaviridae/veterinária , Hepadnaviridae/genética , Hepadnaviridae/isolamento & purificação , Animais , China , Genoma Viral , Hepadnaviridae/classificação , Infecções por Hepadnaviridae/virologia , Filogenia
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